#phd #pancreaticcancer #bioinformatics #metagenomics #researchopportunity #universityofoulu #cancerresearch #translationalresearch #ngs | Silas Kieser PhD Candidate Position in Pancreatic Cancer Metagenomics We're looking for a talented and motivated PhD candidate to join our translational research team at the University of Oulu! **The Opportunity...

www.linkedin.com/posts/silas-...

PhD_postdoc_bioinformatics | Matija Trickovic Our group at the University of Geneva is looking for a new PhD student and/or postdoctoral researcher in bioinformatics to join our work on the microbiome, metabolism and cancer. The person will take ...

New job opening in my previous lab: www.linkedin.com/feed/update/...

What we are looking for
• Strong interest in bioinformatics and disease mechanisms
• Programming experience and familiarity with Unix
• Diploma/MSc degree for PhD applicants or PhD degree for postdoc applicants

Perplexity Perplexity is a free AI-powered answer engine that provides accurate, trusted, and real-time answers to any question.

@garymarcus.bsky.social
If the AI models hallucinate is it a good idea to let robots run free?

www.perplexity.ai/page/study-f...

September 5, 2025 See you next week at #GloMiNe2025! Gut microbiome Gut fungi are associated with human genetic variation and disease risk – Emily P. Van Syoc – Plos Biology The resident gut microbiome modulates the…

New #MicrobiomeDigest is OUT microbiomedigest.com/2025/09/04/s...

• subspecies of the human gut microbiota / @silask.bsky.social

• red grouse microbiota / @microbes4ever.bsky.social

• "Biopolis – into the microbiome" podcast

• invitation for the next week #GloMiNe2025

& more.

Happy Friday!

Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research - PubMed Microbial strains within a single species can exhibit distinct functional characteristics due to variations in gene content and often show individual specificity, which can obscure unbiased associatio...

There are two recent papers that use sourmash in creative ways - and it gladdens my heart! pubmed.ncbi.nlm.nih.gov/40812187/ by @silask.bsky.social et al looks cleverly at human gut subspecies. www.biorxiv.org/content/10.1... by @rayanchikhi.bsky.social et al counts billions of k-mers. Super neat!

This looks really promising! It’s a step in the right direction to drill down to a more function based microbiome analysis while still maintaining taxonomic information.

Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research | Silas Kieser Tričković et al. develop a comprehensive genomic human gut microbiota subspecies catalog by defining operational subspecies units (OSUs) in an unbiased, cohort-independent manner. Panhashome, a sketch...

Link: silask.github.io/publication/...

Because our subspecies are genome-based, we can identify specific genes or mutations that explain differential associations. This provides a direct path to mechanistic understanding.

We found many cases where only one subspecies associates with disease while sibling-subspecies don't. Sometimes no association is detected at species level because opposing subspecies associations cancel each other out.

Why it matters: Subspecies explain disease associations invisible at the species level. For example, in colorectal cancer, subspecies-based ML models consistently outperformed species-level ones.

We created a sourmash-based method for fast & accurate subspecies quantification, enabling large-scale analysis across entire datasets, e.g., the whole SRA.

We built HuMSub: the most comprehensive catalog of human gut microbiota subspecies (5,361 OSUs across 977 species).
We found that 1/3 of species in the human gut have subspecies, most of which we knew nothing about.

Going down to the strain-level isn't useful for most comparative studies, because everyone has person-specific strains for most of their microbes!
We need an intermediate level: Subspecies.

Most microbiome studies stop at the species level. But strains within a species can differ dramatically in function. This obscures associations and limits reproducibility.

New paper out: Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research.

What do you think about our latest pre-print?

1/3 of human microbioal species have, mostly neglected, subspecies.

Human gut microbiota subspecies carry implicit information for in-depth microbiome research
doi.org/10.1101/2025...

My supervisor finally agreed to post a preprint, but he said I should not publicize it on social media.. sad it is revolutionary...

Google voice typing needed 2y to be on the same level as Whisper, but it still cannot distinguish if I speak french or english ,🙄

That will be the future?

I worry less about AI taking my job and more about how much of my job becomes 1) verifying AI-generated claims and 2) figuring out where the AI went wrong and fixing it.

10 INCREDIBLE ways to BOOST your immune system:

The Measles vaccine
The Mumps vaccine
The Rubella vaccine
The Tetanus vaccine
The Diphtheria vaccine
The Polio vaccine
The HPV vaccine
The Pneumonia vaccine
The Hepatitis B vaccine
The Covid-19 vaccine

Postdoctoral Researcher in Bioinformatics of the Human Gut Microbiome Postdoctoral Researcher in Bioinformatics of the Human Gut Microbiome

There’s an open postdoc position in our EIC funded project FIBRE-MATCH at the University of Helsinki, Finland. Further information in the ad.
jobs.helsinki.fi/job-invite/3...

Notion – The all-in-one workspace for your notes, tasks, wikis, and databases. A new tool that blends your everyday work apps into one. It's the all-in-one workspace for you and your team

J’ai regroupé dans ce stack les outils #IA que j’utilise ou que je trouve dignes d’intérêt. 🤖

Cette liste est vouée à évoluer chaque semaine, vu les évolutions incessantes dans le domaine. N'hésitez pas à me dire s'il manque quelque chose 🙂

reymondin.notion.site/144643c1f676...

Vaccines work.

Yes, the church leaders acepted heliocentrism once the evidence convinced them that's better for calculating dates. I don't think any evidence could convince RFK Jr

I find surprising that CLR is not helpful for the associations, rather it is counterproductive.

But then they didn't used the multiplicative replacement for zero-imputing.

GitHub - ncbi/datasets: NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. - ncbi/datasets

I didn't know ncbi actually made a CLI to download genomes and gene sets github.com/ncbi/datasets

A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies - Genome Biology Background In microbiome disease association studies, it is a fundamental task to test which microbes differ in their abundance between groups. Yet, consensus on suitable or optimal statistical method...

Reading "A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies" from our friends in Berlin and in Leiden

Quotes are from the paper (minor edits for space), non quoted text is me

link.springer.com/article/10.1...

Maybe its even too much asked from a supervisor. Be a at top of the biology as well as the bioinformatics

Google doc is the hit.

Would you do it even though MS office is offered by the institution? Do you use a personal Foogle doc account?